The UN's headquarters in Nairobi said that efforts were already under way to secure the freedom of the two employees of the Bangalore-based Genesys International Corporation.
"Latest information suggests they are being held around the town of Jilib, and that clan elders and community leaders who do not condone such abductions are putting pressure on the perpetrators to release the men," it said in a statement.
In Somalia, Genesys undertakes aerial surveys to prepare detailed maps in order to help people affected by floods caused by rises in the water level of the Juba and Shabelle rivers.
Security forces deployed
The district commissioner said he would send security forces to the area where the attack occurred.
"The kidnappers are clan militiamen and the hunt to release the aid workers and capture criminals is ongoing," Hajir Bile Sugal, governor of the Middle Juba region, said.
Aid workers, particularly foreigners, are being targeted more regularly in the Horn of Africa country.
A German aid worker was briefly held by armed men in northern Somalia in mid-February, and three staff of Medecins sans Frontieres were killed by a roadside bomb in January in the southern town of Kismayu, causing the international NGO to pull its foreign staff out of Somalia.
A number of international aid agencies said last month that country had become too dangerous for their workers.
"Attacks on, and killings of aid workers, the looting of relief supplies, and a lack of respect for international humanitarian law by all parties have left two million Somalis in need of basic humanitarian assistance," they said.
The 39 organisations - including Oxfam, World Vision and Save the Children - issued their warning of an impending humanitarian catastrophe in a joint statement ahead of a UN Security Council debate.